A method and apparatus for measuring 3D refractive-index tomograms using a wavefront shaper in ultra-high speed and high precision is provided. The method includes the steps of modifying at least one of an illumination angle and a wavefront pattern of an incident ray through the wavefront shaper and leading the modified incident ray to a sample, measuring a 2D optical field, which passes through the sample, through an interferometry along at least one or more of the incident rays, and obtaining 3D refractive-index tomograms through measured information of the 2D optical field.